[PyMOL] Movie to export

Discussion:

Troels Emtekær Linnet

2011-11-08 20:54:18 UTC

Hi.

I have made a nice little movie in Pymol.
1500 frames.

So now I am wondering what is the best method to export?

At the moment I do export to .png with ray tracing each image.
set ray_trace_frames = 1
That takes a long time.
And what program should I use to pack them together? The easy wasy?

Can it be done faster with the MPEG method?

Best
Troels

Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234

Jason Vertrees

2011-11-08 21:07:14 UTC

Permalink

Hi Troels,

One benefit of the Incentive version of PyMOL is the Files > Save
Movie as ... > MPEG feature. If you don't have that or you want to use
a different compressor that's cool. In the past I had great luck with
mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I
think everyone's using VLC (http://www.videolan.org/) or ffmpeg
(http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel
free to update it.

Cheers,

-- Jason

Post by Troels EmtekÃ¦r Linnet
Hi.
I have made a nice little movie in Pymol.
1500 frames.
So now I am wondering what is the best method to export?
At the moment I do export to .png with ray tracing each image.
set ray_trace_frames = 1
That takes a long time.
And what program should I use to pack them together? The easy wasy?
Can it be done faster with the MPEG method?
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
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Marius Retegan

2011-11-09 09:03:03 UTC

Permalink

On a Linux system you can use the following commands to stick them all together

mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts
bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25
-ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264

This will create a x264 compressed file which you will have to put in
a mp4 container using the following command. You can modify the
bitrate which is now set to 3000 and the framerate 25 fps.

MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4

Best regards,
Marius

--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7Hd0Y

Post by Jason Vertrees
Hi Troels,
One benefit of the Incentive version of PyMOL is the Files > Save
Movie as ... > MPEG feature. If you don't have that or you want to use
a different compressor that's cool. In the past I had great luck with
mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I
think everyone's using VLC (http://www.videolan.org/) or ffmpeg
(http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel
free to update it.
Cheers,
-- Jason

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(o) +1 (603) 374-7120
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Troels Emtekær Linnet

2011-11-09 11:00:18 UTC

Permalink

What codec do I need to install??

MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team
Option x264encopts: Unknown suboption nodct_decimat
success: format: 16 data: 0x0 - 0x0
MF file format detected.
[mf] search expr: *.png
[mf] number of files: 537 (4296)
[demux_mf] file type was not set! trying 'type=png'...
VIDEO: [MPNG] 0x0 24bpp 25.000 fps 0.0 kbps ( 0.0 kbyte/s)
[V] filefmt:16 fourcc:0x474E504D size:0x0 fps:25.000 ftime:=0.0400
Opening video filter: [expand osd=1]
Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.000000, round: 1
==========================================================================
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG)
==========================================================================
Could not find matching colorspace - retrying with -vf scale...
Opening video filter: [scale]
Movie-Aspect is undefined - no prescaling applied.
[swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2
FATAL: Cannot initialize video driver.
Movie-Aspect is undefined - no prescaling applied.
FATAL: Cannot initialize video driver.

Exiting...

Post by Marius Retegan
On a Linux system you can use the following commands to stick them all together
mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts
bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25
-ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264
This will create a x264 compressed file which you will have to put in
a mp4 container using the following command. You can modify the
bitrate which is now set to 3000 and the framerate 25 fps.
MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4
Best regards,
Marius
--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7Hd0Y

------------------------------------------------------------------------------

Post by Jason Vertrees

Post by Troels EmtekÃ¦r Linnet
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Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(o) +1 (603) 374-7120

------------------------------------------------------------------------------

Post by Jason Vertrees
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Marius Retegan

2011-11-09 12:17:08 UTC

Permalink

I used this a long time ago, but after googling for the error "from
bgra to yuv420p" I guess that is a problem with the color space
conversion that memcoder tries to enforce by default. Maybe you could
try imposing the color space by adding -vf "format=bgra", but I think
that the video codec is not going to be happy about that. Try looking
around for other options...

Marius

Post by Troels EmtekÃ¦r Linnet
What codec do I need to install??
MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team
Option x264encopts: Unknown suboption nodct_decimat
success: format: 16 data: 0x0 - 0x0
MF file format detected.
[mf] search expr: *.png
[mf] number of files: 537 (4296)
[demux_mf] file type was not set! trying 'type=png'...
VIDEO: [MPNG] 0x0 24bpp 25.000 fps 0.0 kbps ( 0.0 kbyte/s)
[V] filefmt:16 fourcc:0x474E504D size:0x0 fps:25.000 ftime:=0.0400
Opening video filter: [expand osd=1]
Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.000000, round: 1
==========================================================================
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG)
==========================================================================
Could not find matching colorspace - retrying with -vf scale...
Opening video filter: [scale]
Movie-Aspect is undefined - no prescaling applied.
FATAL: Cannot initialize video driver.
Movie-Aspect is undefined - no prescaling applied.
FATAL: Cannot initialize video driver.
Exiting...

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Tim Schulte

2011-11-09 14:14:34 UTC

Permalink

Hi,
Quick time player 7 pro does a great job for me.
Cheers
Tim

Vitali Stanevich

2011-11-10 05:22:09 UTC

Permalink

have a look at this link:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera

disregard morph part. you can modify script to contain "frames" instead of
"states". i installed ffmpeg from repositories on ubuntu and don't remember
any issues with kodecs.

vitali

Post by Tim Schulte
**
Hi,
Quick time player 7 pro does a great job for me.
Cheers
Tim
Hi.
I have made a nice little movie in Pymol.
1500 frames.
So now I am wondering what is the best method to export?
At the moment I do export to .png with ray tracing each image.
set ray_trace_frames = 1
That takes a long time.
And what program should I use to pack them together? The easy wasy?
Can it be done faster with the MPEG method?
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
------------------------------------------------------------------------------
RSA(R) Conference 2012
Save $700 by Nov 18
Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
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Register now
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Vitali Stanevich

2011-11-10 05:29:36 UTC

Permalink

one more thing: ffmpeg script at that link didn't work for me so i had to
modify it like that

ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg

Post by Vitali Stanevich
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera
disregard morph part. you can modify script to contain "frames" instead of
"states". i installed ffmpeg from repositories on ubuntu and don't remember
any issues with kodecs.
vitali